PB-PENTAdb Help

Last update on Thursday, April 13, 2023

The general scheme used to build PB-PENTAdb is summarized in the diagram below :

pentapeptide database construction process

The database hence contains the following features for each pentapeptide :

  • protein id
  • the PB class
  • the position of the first residue of the pentapeptide in the pdb-style SCOP file
  • the dihedral angles (phi and psi values)
  • the lowest angular rmsd (rmsda) between pentapeptide’s dihedral angles and standard dihedral angles of PBs
  • the secondary structure assignments (from DSSP)
  • a series of 5 values corresponding to the “all atoms” relative solvent accessibility for all 5 residues
  • a series of 5 values corresponding to backbone B factors of 5 residues

Simplified query tool

Input: Enter a valid pentapeptide sequence (5 residues long) in the text area with no space between the residues. You can use the underscore “_” sign to specify “any” residue. You can choose to search in datasets filtered at different sequence similarity cutoffs.

Screen Shot 2015-04-22 at 23.38.14

The results are delivered as followed :

PB-PENTAPEPT

Different links provided on the result page are described in the following figure
Links

SQL Advanced Query

The user can also provide more elaborated queries to the database in the second section of the tool :

SQL Query

Input: Enter a mysql command. DO NOT put a semi colon (;) at the end of your command line.
example : SELECT pb, COUNT(*) AS number FROM mapping100 GROUP BY pb
The table containing the data is called mapping100.
The structure of the table is as follows :

Field id_protein pb aaseq pos psi1 phi2 psi2 phi3 psi3 phi4 psi4 phi5
Type varchar(20) varchar(4) varchar(9) int(11) float float float float float float float int(11)
Field rmsda sec_str rsa1 rsa3 rsa3 rsa4 rsa5
Type float varchar(5) float float float float float

Description of the rmsda100 table in our database :

Field id_protein pb aaseq pos CA_Bfac1 CA_Bfac2 CA_Bfac3 CA_Bfac4
Type varchar(20) varchar(4) varchar(9) int(11) float float float float
Field CA_Bfac5 Bkbone_Bfac1 Bkbone_Bfac2 Bkbone_Bfac3 Bkbone_Bfac4 Bkbone_Bfac5 pb1 rmsda1
Type float float float float float float varchar(4) float
Field pb2 rmsda2
Type varchar(4) float

Results: output is according to user’s query and is downloadable.

Advanced Query

User can choose to fill required fields and leave the other fields which are not required as they are. User can get help about a particular field if he gets the mouse pointer over that field’s text box. e.g. Help about sequence field is shown in the image below.
Advanced Search

User can also choose the fields to be displayed in the result.
Output Fields